int_scale /= 10;        }       else if (strcmp(mtrxname, "id") == 0)        {           matptr = idmat;           mat_xref = def_aa_xref;        }       else if(user_series)        {           matptr=NULL;	   found=FALSE;	   for(i=0;i<matseries.nmat;i++)		if(pcid>=matseries.mat[i].llimit && pcid<=matseries.mat[i].ulimit)		{			j=i;			found=TRUE;			break;		}	   if(found==FALSE)	   {		if(!error_given)		warning("\nSeries matrix not found for sequence percent identity = %d.\n""(Using first matrix in series as a default.)\n""This alignment may not be optimal!\n""SUGGESTION: Check your matrix series input file and try again.",(int)pcid);		error_given=TRUE;		j=0;	   }if (debug>0) fprintf(stdout,"pcid %d  matrix %d\n",(pint)pcid,(pint)j+1);           matptr = matseries.mat[j].matptr;           mat_xref = matseries.mat[j].aa_xref;/* this gives a scale of 0.5 for pcid=llimit and 1.0 for pcid=ulimit */           scale=0.5+(pcid-matseries.mat[j].llimit)/((matseries.mat[j].ulimit-matseries.mat[j].llimit)*2.0);        }       else         {           matptr = usermat;           mat_xref = aa_xref;        }if(debug>0) fprintf(stdout,"pcid %3.1f scale %3.1f\n",pcid,scale);      	maxres = get_matrix(matptr, mat_xref, matrix, negative, int_scale);      if (maxres == 0)        {           fprintf(stdout,"Error: matrix %s not found\n", mtrxname);           return(-1);        }          if (negative) {              gapcoef1 = gapcoef2 = 100.0 * (float)(gap_open);              lencoef1 = lencoef2 = 100.0 * gap_extend;	  }          else {          if (mat_avscore <= 0)              gapcoef1 = gapcoef2 = 100.0 * (float)(gap_open + logmin);	  else              gapcoef1 = gapcoef2 = scale * mat_avscore * (float)(gap_open/(logdiff*logmin));              lencoef1 = lencoef2 = 100.0 * gap_extend;	 }    }if (debug>0){fprintf(stdout,"matavscore %d\n",mat_avscore);fprintf(stdout,"Gap Open1 %d  Gap Open2 %d  Gap Extend1 %d   Gap Extend2 %d\n",   (pint)gapcoef1,(pint)gapcoef2, (pint)lencoef1,(pint)lencoef2);fprintf(stdout,"Matrix  %s\n", mtrxname);}  profile1 = (sint **) ckalloc( (prf_length1+2) * sizeof (sint *) );  for(i=0; i<prf_length1+2; i++)       profile1[i] = (sint *) ckalloc( (LENCOL+2) * sizeof(sint) );  profile2 = (sint **) ckalloc( (prf_length2+2) * sizeof (sint *) );  for(i=0; i<prf_length2+2; i++)       profile2[i] = (sint *) ckalloc( (LENCOL+2) * sizeof(sint) );/*  calculate the Gap Coefficients.*/     gaps = (sint *) ckalloc( (max_aln_length+1) * sizeof (sint) );     if (switch_profiles == FALSE)        calc_gap_coeff(alignment, gaps, profile1, (struct_penalties1 && use_ss1), gap_penalty_mask1,           (sint)0, nseqs1, prf_length1, gapcoef1, lencoef1);     else        calc_gap_coeff(alignment, gaps, profile1, (struct_penalties2 && use_ss2), gap_penalty_mask2,           (sint)0, nseqs1, prf_length1, gapcoef1, lencoef1);/*  calculate the profile matrix.*/     calc_prf1(profile1, alignment, gaps, matrix,          aln_weight, prf_length1, (sint)0, nseqs1);if (debug>4){extern char *amino_acid_codes;  for (j=0;j<=max_aa;j++)    fprintf(stdout,"%c    ", amino_acid_codes[j]); fprintf(stdout,"\n");  for (i=0;i<prf_length1;i++)   {    for (j=0;j<=max_aa;j++)      fprintf(stdout,"%d ", (pint)profile1[i+1][j]);    fprintf(stdout,"%d ", (pint)profile1[i+1][gap_pos1]);    fprintf(stdout,"%d ", (pint)profile1[i+1][gap_pos2]);    fprintf(stdout,"%d %d\n",(pint)profile1[i+1][GAPCOL],(pint)profile1[i+1][LENCOL]);   }}/*  calculate the Gap Coefficients.*/     if (switch_profiles == FALSE)        calc_gap_coeff(alignment, gaps, profile2, (struct_penalties2 && use_ss2), gap_penalty_mask2,           nseqs1, nseqs1+nseqs2, prf_length2, gapcoef2, lencoef2);     else        calc_gap_coeff(alignment, gaps, profile2, (struct_penalties1 && use_ss1), gap_penalty_mask1,           nseqs1, nseqs1+nseqs2, prf_length2, gapcoef2, lencoef2);/*  calculate the profile matrix.*/     calc_prf2(profile2, alignment, aln_weight,           prf_length2, nseqs1, nseqs1+nseqs2);     aln_weight=ckfree((void *)aln_weight);if (debug>4){extern char *amino_acid_codes;  for (j=0;j<=max_aa;j++)    fprintf(stdout,"%c    ", amino_acid_codes[j]); fprintf(stdout,"\n");  for (i=0;i<prf_length2;i++)   {    for (j=0;j<=max_aa;j++)      fprintf(stdout,"%d ", (pint)profile2[i+1][j]);    fprintf(stdout,"%d ", (pint)profile2[i+1][gap_pos1]);    fprintf(stdout,"%d ", (pint)profile2[i+1][gap_pos2]);    fprintf(stdout,"%d %d\n",(pint)profile2[i+1][GAPCOL],(pint)profile2[i+1][LENCOL]);   }}  aln_path1 = (char *) ckalloc( (max_aln_length+1) * sizeof(char) );  aln_path2 = (char *) ckalloc( (max_aln_length+1) * sizeof(char) );/*   align the profiles*//* use Myers and Miller to align two sequences */  last_print = 0;  print_ptr = 1;  sb1 = sb2 = 0;  se1 = prf_length1;  se2 = prf_length2;  HH = (lint *) ckalloc( (max_aln_length+1) * sizeof (lint) );  DD = (lint *) ckalloc( (max_aln_length+1) * sizeof (lint) );  RR = (lint *) ckalloc( (max_aln_length+1) * sizeof (lint) );  SS = (lint *) ckalloc( (max_aln_length+1) * sizeof (lint) );  gS = (lint *) ckalloc( (max_aln_length+1) * sizeof (lint) );  displ = (sint *) ckalloc( (max_aln_length+1) * sizeof (sint) );  score = pdiff(sb1, sb2, se1-sb1, se2-sb2, profile1[0][GAPCOL], profile1[prf_length1][GAPCOL]);  HH=ckfree((void *)HH);  DD=ckfree((void *)DD);  RR=ckfree((void *)RR);  SS=ckfree((void *)SS);  gS=ckfree((void *)gS);  ptracepath( &alignment_len);    displ=ckfree((void *)displ);  add_ggaps();  for (i=0;i<prf_length1+2;i++)     profile1[i]=ckfree((void *)profile1[i]);  profile1=ckfree((void *)profile1);  for (i=0;i<prf_length2+2;i++)     profile2[i]=ckfree((void *)profile2[i]);  profile2=ckfree((void *)profile2);  prf_length1 = alignment_len;  aln_path1=ckfree((void *)aln_path1);  aln_path2=ckfree((void *)aln_path2);  NumSeq = 0;  for (j=0;j<nseqs;j++)    {       if (group[j+1]  == 1)         {            seqlen_array[j+1] = prf_length1;	    realloc_seq(j+1,prf_length1);            for (i=0;i<prf_length1;i++)              seq_array[j+1][i+1] = alignment[NumSeq][i];            NumSeq++;         }    }  for (j=0;j<nseqs;j++)    {       if (group[j+1]  == 2)         {            seqlen_array[j+1] = prf_length1;            seq_array[j+1] = (char *)realloc(seq_array[j+1], (prf_length1+2) * sizeof (char));	    realloc_seq(j+1,prf_length1);            for (i=0;i<prf_length1;i++)              seq_array[j+1][i+1] = alignment[NumSeq][i];            NumSeq++;         }    }  for (i=0;i<nseqs1+nseqs2;i++)     alignment[i]=ckfree((void *)alignment[i]);  alignment=ckfree((void *)alignment);  aln_len=ckfree((void *)aln_len);  gaps=ckfree((void *)gaps);  return(score/100);}static void add_ggaps(void){   sint j;   sint i,ix;   sint len;   char *ta;   ta = (char *) ckalloc( (alignment_len+1) * sizeof (char) );   for (j=0;j<nseqs1;j++)     {      ix = 0;      for (i=0;i<alignment_len;i++)        {           if (aln_path1[i] == 2)              {                 if (ix < aln_len[j])                    ta[i] = alignment[j][ix];                 else                     ta[i] = ENDALN;                 ix++;              }           else if (aln_path1[i] == 1)              {/*   insertion in first alignment...*/                 ta[i] = gap_pos1;              }           else              {                 fprintf(stdout,"Error in aln_path\n");              }         }       ta[i] = ENDALN;              len = alignment_len;       alignment[j] = (char *)realloc(alignment[j], (len+2) * sizeof (char));       for (i=0;i<len;i++)         alignment[j][i] = ta[i];       alignment[j][len] = ENDALN;       aln_len[j] = len;      }   for (j=nseqs1;j<nseqs1+nseqs2;j++)     {      ix = 0;      for (i=0;i<alignment_len;i++)        {           if (aln_path2[i] == 2)              {                 if (ix < aln_len[j])                    ta[i] = alignment[j][ix];                 else                     ta[i] = ENDALN;                 ix++;              }           else if (aln_path2[i] == 1)              {/*   insertion in second alignment...*/                 ta[i] = gap_pos1;              }           else              {                 fprintf(stdout,"Error in aln_path\n");              }         }       ta[i] = ENDALN;              len = alignment_len;       alignment[j] = (char *) realloc(alignment[j], (len+2) * sizeof (char) );       for (i=0;i<len;i++)         alignment[j][i] = ta[i];       alignment[j][len] = ENDALN;       aln_len[j] = len;      }         ta=ckfree((void *)ta);   if (struct_penalties1 != NONE)       gap_penalty_mask1 = add_ggaps_mask(gap_penalty_mask1,alignment_len,aln_path1,aln_path2);   if (struct_penalties1 == SECST)       sec_struct_mask1 = add_ggaps_mask(sec_struct_mask1,alignment_len,aln_path1,aln_path2);        if (struct_penalties2 != NONE)       gap_penalty_mask2 = add_ggaps_mask(gap_penalty_mask2,alignment_len,aln_path2,aln_path1);   if (struct_penalties2 == SECST)       sec_struct_mask2 = add_ggaps_mask(sec_struct_mask2,alignment_len,aln_path2,aln_path1);if (debug>0){  char c;  extern char *amino_acid_codes;   for (i=0;i<nseqs1+nseqs2;i++)     {      for (j=0;j<alignment_len;j++)       {        if (alignment[i][j] == ENDALN) break;        else if ((alignment[i][j] == gap_pos1) || (alignment[i][j] == gap_pos2))  c = '-';        else c = amino_acid_codes[alignment[i][j]];        fprintf(stdout,"%c", c);       }      fprintf(stdout,"\n\n");     }}}                  static char * add_ggaps_mask(char *mask, int len, char *path1, char *path2){   int i,ix;   char *ta;   ta = (char *) ckalloc( (len+1) * sizeof (char) );       ix = 0;       if (switch_profiles == FALSE)        {              for (i=0;i<len;i++)           {             if (path1[i] == 2)              {                ta[i] = mask[ix];                ix++;              }             else if (path1[i] == 1)                ta[i] = gap_pos1;           }        }       else        {         for (i=0;i<len;i++)          {            if (path2[i] == 2)             {               ta[i] = mask[ix];               ix++;             }            else if (path2[i] == 1)             ta[i] = gap_pos1;           }         }       mask = (char *)realloc(mask,(len+2) * sizeof (char));       for (i=0;i<len;i++)         mask[i] = ta[i];       mask[i] ='\0';